It appears you have two different problems that are likely not related. First of all, I overlooked the obvious. Since the transmission was removed, it is almost certain the battery had to be disconnected. At that point the Engine Computer lost its memory, most importantly, "minimum throttle". Until it relearns that, idle speed will be too low for reliable starting, you won't get the normal "idle flare-up" to 1500 rpm at engine start-up, and it will typically stall when coming to a stop.
To get the engine to start you may need to hold the gas pedal down about 1/4". To meet the conditions for the relearn to take place, drive at highway speed with the engine warmed up, then coast for at least seven seconds without touching the pedals.
If the intermittent clicking you're hearing is a rather loud single click each time you turn the ignition switch to "crank", the first thing I'd suspect is a loose cable connection on the starter. The mechanic may have removed it to get it out of the way for removing the transmission, and forgot to tighten it.
Wednesday, February 20th, 2013 AT 8:14 PM